Visual examination of mass spectrometry data is necessary to assess data quality and to facilitate data exploration. Graphics provide the means to evaluate spectral properties, test alternative peptide/protein sequence matches, prepare annotated spectra for publication, and fine-tune parameters during wet lab procedures. Visual inspection of LC-MS data is hindered by proteomics visualization software designed for particular workflows (e.g. bottom-up or top-down analyses; support for ThermoFisher raw files or XML-based, etc.) or vendor specific tools without open-source code. We built PSpecteR, an open-source and interactive R Shiny web application to address these issues, with support for several steps of proteomics data processing, including: reading various mass spectrometry files, running open-source database search engines, labelling spectra with fragmentation patterns, testing post-translational modifications, plotting where identified fragments map to reference sequences, and visualizing algorithmic output and metadata. All figures, tables, and spectra are exportable within one easy-to-use graphical user interface. Our current software provides a flexible and modern R framework to support fast implementation of additional features. The open-source code is readily available (https://github.com/EMSL-Computing/PSpecteR), and a PSpecteR Docker container (https://hub.docker.com/r/emslcomputing/pspecter) is available for easy local installation.
There are two version of PSpecteR:
PSpecteR: The full version of the application which includes the ability to run MS-GF+ and MSPathFinder.
PSpecteR Light: A simpler version of the application which does not include MS-GF+ and MSPathFinder. It also does not include file autodetection and loading.
Upload Data: Upload either an XML-based (.mzML, .mzXML) MS file, or a ThermoFisher (.raw) file. For identification data, currently only mzid data is supported. FASTA files are optional. Example datasets are included within the application.
MS & XIC: Visualize peptide and protein identifications overlayed on experimental mass spectra data. Extracted ion chromatograms are also calculated and visualized.
Test and Visualize PTMs: Use ProForma strings to test the fit of alternative proteoforms. There are widgets and shorthand options to test multiple modifications quickly. Any unique modifications can be added in the glossary.
Protein Coverage: Visualize where identified peptides overlay on protein sequences.
Additional Plots: There are 2 available plots - plotting metadata, and ProMex (part of the MSPathFinder suite) feature identification data.
Glossary: Append the glossary of post-translational modifications with your own.
All data from the application can be exported with widgets in the sidebar, and all plots are resizable with a draggable symbol on the bottom right hand corner. Snapshots of plots can be taken within the plot windows with the camera icon. For higher quality images, simply make the image larger.
This page allows the user to upload:
A required mass spectrometry file (MS): mzML, mzXML, or Thermo Fisher raw
An optional protein ID file (ID): mzid
An optional protein database file (FA): fasta
You may also choose the test files at the bottom of the “Upload Data” page. There is also a description mode with pop-ups that we suggest new users try out.
Click “Browse” to open your system’s file explorer to upload your data.
Click a dropdown menu to set the output directory or upload an MS, ID, or FA file. Use the “Search Folders” button to select a file,
or type in an acceptable file path, which will give a check mark for a correct path or a red X for an incorrect path. Click “Use Path” to load the file, or “Clear Path” to remove it. When typing in a MS file path, if the ID and FA file paths have the same name, directory, and correct extension, they will autofill.